When a passing comet abruptly changes course and hurtles towards Earth, there is widespread panic and distress as people prepare for Armageddon. However, the comet does not crash: instead, it slows down, hovers, and eventually touches down on a lake in the Pacific Northwest. Finally, 4400 people emerge from a blinding white light, people from all different ages and walks of life who have been presumed dead or missing - and none aged even a day from when they were last seen. It's as if a giant time capsule full of people has been opened up, unaltered and untouched by time. Although not immediately evident, it soon becomes apparent that The 4400 have each been returned with a special power as they unwittingly begin to exhibit abilities including superhuman strength, healing touch, and clairvoyance. Eager to revisit memories from their past and reunite with those they left behind, two worlds collide as 4400 people acclimated to living in the past are forced to deal with the new challenges of living in the present.

A new federal division agency of Homeland Security called NTAC (National Threat Assessment Command) is formed to follow The 4400. Tom Baldwin, a crime investigator, and Diana Skouris, a bio medic, are one of the many agents. Tom's involvement is personal: his nephew Shawn was one of the 4400 people abducted - and, if not for Shawn, his son Kyle would have been abducted instead.

3x6: Graduation Day recap: After entering NTAC, Tom is told by Diana that they "need to get started." Tom has no idea what she is talking about. He follows her into an interrogation room. Inside is Isabelle, who is dressed in a prisoner uniform, and in front of her is the syringe containing the substance that can kill her. Diana tells Tom that he has to do this, but he is hesitant. However, Isabelle also states that he must kill her because she may be bad and eventually kill millions of people. Tom reluctantly injects Isabelle with the substance. As she starts to scream in pain, Tom wakes up in his bed. He then goes to his closet and removes the syringe from a safe.
Meanwhile, blood is dripping into a sink, and it is revealed that it is coming from Shawn. His arms are covered in blood, and he is muttering to himself that he can't find the bug inside of him. He then walks off, stating that he's going to get an x-ray of his body. A little while later, as Maia is chasing a friend in the woods outside of the 4400 Center, she runs straight into Shawn and falls down. Her leg is injured, so Shawn volunteers to fix it. However, he instead begins draining her of her life! Luckily, employees of the Center are nearby and rescue her. A confused Shawn explains that he was trying to heal her.
As Diana later visits Maia in the 4400 Center's clinic, Richard takes Tom to Shawn's room, which is trashed. A worried Isabelle enters, wanting to see Shawn. Richard tells her that she can't see him right now. He then introduces her to Tom, who is nervous around her. Isabelle notices that he is staring at her and asks why he is doing so, but Shawn's psychiatrist returns from Shawn's bedroom before Tom can respond. The psychiatrist explains that Shawn is experiencing persistent and powerful auditory hallucinations, which are contributing to his delusions. His symptoms are consistent with the onset of disorganized schizophrenia. However, the diagnosis is unusual, since schizophrenia is usually gradual instead of sudden.
A little while later, Richard reveals to Tom and Diana about Daniel Armand's threat from the previous week, and he suspects that Armand has to do with Shawn's sudden illness. Diana promises to investigate but tells Richard and Matthew Ross that Shawn needs to be temporarily committed for the protection of others. Isabelle then enters and forbids them from locking Shawn up. However, Richard agrees to commit Shawn to a private hospital until everything is cleared up.
Elsewhere, Alana is speaking to a teen named Todd Barstow, who disappeared on August 29, 1995. She explains that since the 4400 children missed years from their family life, she can use her ability to allow them to relive their lost years. She offers to let him see his brother that was born while he was gone and to allow them to form a relationship. However, Todd replies that she should worry more about helping herself. Alana questions this, and he states that she has a "rage" inside of her that was created by the deaths of her husband and son. She asks how he knows about the hit-and-run accident, and Todd explains that it's part of his ability. As Todd then leaves to go back to class, he tells Alana that she has a right to be mad, since the person who killed her family is still at large.
At NTAC, Tom and Diana are investigating Shawn's illness. Although Diana puts out the idea that Shawn's schizophrenia may be normal, Tom still believes that the Nova Group did it. Meanwhile, at the request of Matthew, Richard meets in the woods with Zachary Gidlund, who disappeared on November 10, 1966. Zachary tells Richard that Jane Nance, a friend from quarantine, recently asked him to join her for dinner. During it, she asked him many questions, and he suspects that she was trying to recruit him for the Nova Group. Zachary gives him her name, and Richard thanks him. As they go their separate ways, Zachary is met by Isabelle. Elsewhere, Alana meets up with Todd and asks how he knew about her private thoughts. Todd explains that if someone that he's talking to is feeling something strong, he feels and sees it, too. Although he only sees fragments, he gives her the name of the drunk driver: Keane Driscoll.
Matthew catches Isabelle packing Shawn's clothes, and she explains that she is taking Shawn out of the hospital. Matthew tries to stop her from acting on the tip about the Nova Group and reminds her about her purpose, which is to eliminate the 4400! According to him, the coming catastrophe is actually the 4400. When Isabelle then starts to leave, Matthew warns her that she isn't ready to be alone and still needs his guidance. However, Isabelle begins using her powers to kill him. As he dies, she states that she no longer needs him and that it's "graduation day."
As Isabelle takes Shawn out of the Abendson Psychiatric Care Facility, NTAC locates Jane Nance, who disappeared on October 17, 1980. Jane's home is filled with animals, and it appears that her ability is to communicate with animals. There is a knock at the door, so Jane answers it. However, no one is there. When she then closes the door and turns around, she is face to face with Isabelle. Meanwhile, Alana stops by an Alcoholics Anonymous meeting that is being led by Keane Driscoll.
As NTAC enters Jane's home and finds her mauled to death by her pets, Richard learns of Matthew's demise, which doctors think was caused by a stroke. Tom and Diana talk to Richard and reveal that they suspect that Isabelle is connected to the deaths. He doesn't believe that his daughter could be responsible, but he promises to try to convince Isabelle to come back to the Center if she calls. Elsewhere, at the Alcoholics Anonymous meeting, Alana speaks to Keane. He reveals to her that he first started coming to the meetings about nine years earlier, after being involved in a car accident. However, he has little memory of the incident, and he has no idea that he killed anyone.
At NTAC, Tom tells Diana that they've put a trace on Shawn's and Richard's phones so that they can listen in if Isabelle calls. The two then talk about Isabelle. Diana reveals her fears, and Tom states that Isabelle is a whole new category of 4400. Agent Garrity then interrupts to tell them that Shawn's car has been located. As Diana leaves to go after Shawn and Isabelle, Tom stops by his home to get the syringe. Elsewhere, Isabelle takes Shawn with her to an auto garage owned by Jorge Molina, who disappeared on March 24, 1975.
Tom later returns home, finding Alana waiting for him in the living room. He informs her that Shawn's car was found abandoned. She then tells him about Todd Barstow and his abilities, as well as the fact that she knows the identity of the drunk driver. After Tom is told about her visiting the driver, to which he tells her to not do again, his cellphone rings. He answers, and a short while later, he arrives at Molina's garage, which has been burned to the ground. There are some burnt remains inside that are believed to be Molina. The origin of the fire is unknown, although Tom and Diana suspect that Isabelle caused it.
At the 4400 Center, Richard is awakened by a call from Isabelle. She promises that it's almost over and that Daniel Armand is causing Shawn's schizophrenia. She and Shawn are about to go to Armand's home. Afraid that she is in too much trouble, Isabelle asks if she will be able to return to the Center. Richard replies that he doesn't know, and he convinces her to tell him where she is going. NTAC intercepts the call, and Tom and Diana head to Armand's house. In Armand's basement, Isabelle has him tied to a chair. She then gets him to cure Shawn of his illness. Shawn returns to normal, with no memory of what happened. Not wanting to kill Armand, Shawn begins to get Isabelle to leave with him, but Armand reveals what Isabelle did to the Nova Group to locate him. However, she replies that she didn't exactly kill anyone; she merely turned their abilities against them. Against Shawn's pleas to stop, Isabelle begins turning Armand's abilities against himself.
Watching the now schizophrenic Armand, Shawn asks Isabelle why she did that. She explains that if they just left him, he could attack again. After being told that she would kill a hundred people to protect him, Shawn questions who she is. Before an upset Isabelle can reply, they hear NTAC arriving. Outside, Richard convinces Tom and Diana to let him speak to Isabelle before barging in. Richard soon arrives in the basement and learns that Isabelle wants to fight NTAC, so he tries to get her to come out willingly. She states that after all she did, Shawn now hates her, but he and Richard reveal that they're only scared of her. The trio then exits, and NTAC goes in to get Armand.
Later at NTAC, Tom and Diana watch as Isabelle is released due to a lack of evidence. Diana states her fears of Isabelle doing something even worse. Meanwhile, Alana shows Keane a newspaper clipping about the deaths of her husband and son. He doesn't understand why she's showing him this, but she reveals that he killed them while drunk. Keane claims that he's a different man now, but Alana states that she won't let him forget what he did. At the 4400 Center, Isabelle goes to her room and finds Tom waiting for her. He tells her that they need to talk. She agrees, so after revealing that some people want him to kill her, he asks her why they want him to. Isabelle sees the syringe and asks who gave it to him. Tom doesn't tell her who gave it to him, but he does say that the woman who did called her "evil." Isabelle then reveals what Matthew tried to get her to do and why she killed him; she also adds that she turned her back on being bad. Isabelle doubts that Tom can bring himself to murder, so she holds out her arm. He almost injects her with it, but he stops himself because he wants to make sure that killing her is the right thing to do.
At the 4400 Center, Todd shows Alana a newspaper article about Keane, who is in critical condition after being involved in an accident; his blood alcohol level was three times the legal limit. He fears that he caused it to happen, but Alana tells him that she did it. Elsewhere, Isabelle has an appointment with Dennis Ryland... read more.

3x5: Gone (2) recap: Marco stops by Diana's apartment for dinner and brings her flowers. He notices that there are three plates set and asks who the third person is. She replies that it's only the two of them and also finds it strange that she set it for three. Meanwhile, Tom and Alana are in a fantasy world in which they are driving a fancy car along the countryside. However, a young girl resembling Maia suddenly runs in front of the road, and the car hits her. The two get out of the car to check on her, but there is no body. They then see her walking down the road, so they follow. To their shock, the girl has no face. After seeing that, the two return to reality and question who the girl was.
Alana explains to Tom that she creates her fantasy worlds from memories, so she probably pulled up a fragmented memory. Elsewhere, Isabelle and Shawn, in formal attire, are making out in a staircase. However, Devon sees them and walks away, embarrassed. Isabelle reassures Shawn that Devon won't tell Richard because she would be too afraid, but Shawn states that word will spread and eventually get to Richard.
At NTAC, Tom is drawing a picture of the faceless girl. Jarvis enters and informs him that a 4400 named Christopher Dubov was attacked outside of his home. Jarvis thinks it may be a hate crime, but Tom suggests that his occupation as a lawyer in a major mergers and acquisitions firm is the cause because he has put many people out of work. Diana then arrives and has many magazines in her bag. Tom questions her about it, but she explains that it's for a "project" that she is working on.
Later, Tom and Diana question Christopher Dubov, who disappeared on June 29, 1999. Since being taken off of the promicin inhibitor, he has gained the ability to smell pheromones. Dubov explains that his son, Michael, attacked him for setting his mother up with her new husband. Diana sees photos of Dubov and Michael, and she comments that they look very happy together. Dubov tells her that the photos were taken when Michael was 10, and Diana strangely replies that "10" is a great age. Dubov then states that he isn't going to press charges. He is instead going to set Michael up with a waitress at a local bar. After leaving Dubov's office, Tom and Diana get into their car. Diana suddenly starts crying after thinking about how much Michael must have missed his father during his five-year absence.
At the 4400 Center, Shawn confesses to Richard about his relationship with Isabelle, and Richard is furious. He orders Shawn to stay away from her, but Shawn states that he can't promise that. Matthew Ross then enters and stops the argument, siding with Richard. That night, Alana and Tom are in a fantasy world in which they are at home, about to go fishing with Kyle. Tom calls for Kyle and heads for the stairs. To his surprise, Maia is on the steps. He recognizes her as the girl that he hit in the other fantasy. She states her name and informs him that she is in his fantasy because he wants her to be there. After Tom realizes that he wants to remember her, he and Alana return to reality.
The next day, Tom visits Diana, who called in sick. After talking to her at the door, he suspects something is wrong and enters, finding magazine clippings everywhere. She explains that it's her "project." Tom finds a picture of Maia's face, taped together from pieces of other faces. Diana states that she was up all night doing it, and she fears that she is going crazy. However, Tom replies that he has seen the girl in his fantasies, and the girl's name is Maia. After hearing this, Diana takes Tom into another room, where the name "Maia" is formed on the wall from clippings of girls.
Tom tells Diana that there is no "Maia" in any of their case files, and he suggests that they may have met her at one of Agent Garrity's barbecues. However, Diana replies that she knows Maia more than that. When Tom then says that the only place that Maia currently exists is in his fantasy worlds, Diana requests that he have Alana take her to one. Meanwhile, Richard walks in on Isabelle brilliantly playing a piano, and she reveals that it's her first time playing! He then sits down next to her to talk. Richard requests that she stop sleeping with Shawn for the time being, but she refuses. Isabelle then departs to find someone at the Center with a cello.
At Tom's house, Diana tells Alana to take them to her apartment. However, when the fantasy starts, they instead arrive in a courthouse. The door in front of them opens, and Maia emerges. She takes Diana into the judge's office, where Diana legally adopts her. When Maia hugs her, Diana's memories return. The fantasy then ends, and Diana reveals what has happened; Tom believes her.
At the 4400 Center, Richard receives a call from Daniel Armand of the Nova Group. Armand wants to meet to form a truce, or Shawn will be in danger. Richard informs Matthew Ross and Shawn. Shawn doesn't want him to go, but Richard is still considering it. At NTAC, Jarvis tells Tom and Diana that Maia and the other missing kids aren't 4400's. However, after Diana explains that they've been wiped from their memories and records, Tom reveals that, within the past week, the children's families have been haunted by phantom memories of their children lost long ago. Marco then enters and states that he has found the kids. He shows them a photo from 1893, and Tyler Downing is in it! Tyler graduated first in his class from Yale University in engineering. In 1915, he helped develop synthetic petroleum, which cars currently run on!
A picture of Lindsey Hammond in 1918 is shown. She was adopted by rocket pioneer Robert Goddard, and she invented the composite materials used in the first lunar colonies. Diana asks about Maia, and Marco explains that she was harder to track down. He shows a picture of Maia's diary that is dated 1847. She wrote in it while part of a wagon train crossing the Oregon Trail. Unfortunately, she died of smallpox in October of the same year at the age of 25. Meanwhile, Shawn tells Isabelle that they have to stop seeing each other. However, she doesn't want the relationship to end, so, according to her, it won't.
Diana later comes to Tom's home during a storm. She begs Alana to let her see Maia again, so Alana does. However, when the fantasy starts, Diana is in her apartment, and Alana is nowhere to be seen. Maia then enters the room and asks if they can have pancakes. In the real world, Tom returns to the living room, finding Alana and Diana unconscious on the floor. Tom wakes Alana up and finds that she is bleeding from her nose. Alana explains that she tried to bring them back to reality, but Diana somehow broke away and is still dreaming. Tom questions why Diana hasn't come back yet, so Alana suggests that Diana is happy there with Maia and has no intention of returning.
Tom and Alana take Diana to the hospital, and they are later told by a doctor that her brain activity, heart rate, breathing, and blood pressure are far beyond normal and are steadily increasing. If her rates aren't slowed down, Diana will die. After the doctor leaves, Tom and Alana enter Diana's mind. Diana knows that she will die if she doesn't leave, but she doesn't care. When Diana refuses to let the fantasy end, the duo leaves.
At the 4400 Center, Richard is about to meet with Armand. He passes Isabelle in the hall and wants to talk to her. She states that he has nothing to do with her relationship with Shawn. When he refuses to stay out of her business, she starts to kill him with her powers! Matthew seems happy as he watches, but Isabelle then stops her actions and apologizes with a hug.
At the hospital, Tom tells a comatose Diana that he has a plan. He then goes to a bridge and ties a noose attached to the bridge around his neck. Tom jumps but suddenly finds himself in the future. When Sarah enters, Tom demands that she return the children, or she may as well just return him to where he was. Sarah obeys and extracts them, but she warns that doing so has threatened both his time and the future. She explains that the original 4400's existence hasn't stopped the catastrophe because their enemies, who prefer that history remain the same, are more resourceful than imagined. To stop the 4400, the enemy let loose an evil into Tom's time. The 4400 children were sent farther back in time to combat the evil force, so extracting them will negate any good effects they had. Tom questions if there is another way to stop the evil, and Sarah replies that there is: Tom himself. He promises to do whatever he has to do if the children are returned, so Sarah reluctantly takes him up on his offer. However, before doing so, she states that he will regret his decision.
Tom arrives back in the present in front of Sarah's home. He enters and finds an envelope with his name on it above the fireplace. When he hears noises coming from upstairs, he puts the envelope in his pocket and then investigates. He soon comes upon the missing children. Meanwhile, when Richard fails to meet with Armand, the Nova Group leader remotely uses his ability on Shawn. At the 4400 Center, Shawn pulls out a box cutter, and after cutting open his bed, he begins cutting his arm.
In Diana's fantasy world, she is tucking Maia in bed. Maia gets her to shut her eyes and hold her hand. Diana obeys and awakens in the hospital to find the real Maia holding her hands. Tom then leaves the room and opens the envelope. In it is a syringe with a vial full of a white substance, as well as a note reading "Kill Isabelle.".. read more.

3x4: Gone (1) recap: In the morning, Shawn and Isabelle are naked in bed, making out. There's a knock on the door, so after pulling on a robe, Shawn answers it. Richard tells him that since he's taken over Lily's position in the foundation, he's been looking at financial reports. He then asks Shawn if he remembers what some of the large transactions from the foundation's account were for, but Shawn lies and states that he doesn't.
Meanwhile, Alana and Tom go to the 4400 Center for a barbeque. Many of the 4400 there resent Tom for working at NTAC, but he and Alana then run into Heather Tobey, the 4400 that brought out her students' artistic potential. Heather reveals that she's now a teacher at the 4400 Center's school. She mentions that Alana will be, too, so Alana tells Tom that she's been offered a job to work with the children at the 4400 Center's school.
Elsewhere, Maia and Diana are in a parking garage. Maia forgot her sweater, so she starts to go back to get it. However, she suddenly has a vision and states to Diana, "You're gonna forget me." Diana reassures her that she'll never forget her. Maia then heads back to their apartment to retrieve her sweater. When Maia is gone for a long time, Diana goes to check on her. She finds Maia in the living room with a woman that claims to be Sarah Rutledge, Maia's sister!
Maia and Sarah look through a photo album and reminisce. Diana then makes Maia leave the room so that she and Sarah can talk. Diana, who had searched for Sarah for a long time, is angry at her for not coming for Maia when she was first returned. For Maia's safety, she then refuses to let Sarah see Maia until she can prove that she is really her sister.
At Tom's home, he is furious with Alana for not telling him about the job offer. She apologizes and then explains that the 4400 Center wants her to use her ability to help the children. Meanwhile, at a hospital, Shawn is about to perform a group healing on children. A disguised member of the Nova Group then throws red paint on him and calls him a traitor; security grabs the 4400 and takes him away. Elsewhere, at NTAC, after Diana talks to Tom about Sarah, the duo is told by Jarvis to investigate the disappearance of 4400 Lindsey Hammond.
Meanwhile, at the 4400 Center, Matthew Ross shows Richard and Shawn a postcard from the Nova Group. After being asked why he has suddenly become a target, Shawn explains that he donated money to the Nova Group before they turned deadly. Richard is furious that Shawn took money from the foundation, and Shawn apologizes. Elsewhere, Maia is in the backyard of the home of classmate Amy Paspalis, who disappeared on July 23, 1999. The two are playing badminton. Sarah then appears. At NTAC, Tom informs Diana that the DNA tests show that Sarah isn't Maia's sister, so the two go to Amy's house. However, they are told by Amy that Maia left with her sister.
An Amber Alert is put out for Maia, and unfortunately, Sarah's true identity can't be found by NTAC. Meanwhile, Maia and Sarah are walking on a sidewalk. When asked about her abilities since being taken off the promicin inhibitor, Maia explains that she's learning to focus her premonitions now; they rarely sneak up on her. The two then arrive at Sarah's new house, and she shows Maia a room identical to how Maia kept hers before she was first taken.
As Matthew talks to Richard about him sharing power with Shawn at the 4400 Center, Marco points out recurring butterflies in Maia's diaries. He also reveals that he read how he is going to die. Marco then shows them an entry about Diana going to pick her up from Amy's house but already being gone; she is in a circle with Tyler Downing, a classmate of Maia's. Diana and Tom speak to Tyler, but he claims that he doesn't know anything about Maia's disappearance or the "circle."
At Sarah's house, Maia leaves her room to ask Sarah when Diana is going to pick her up. However, the hallway door is locked. Lindsey Hammond, who disappeared on November 23, 1979, and a few other children emerge from other rooms and tell Maia that there's no point in calling for Sarah, because she never comes. Maia is told that, like them, she is part of Sarah's "collection." The hallway door then becomes unlocked, so the kids all run back into their rooms. Maia secretly watches as a crying Tyler is brought in.
Tom arrives home and finds Alana practicing her ability on Heather. Alana reveals to him that she is going to accept the 4400 Center's job offer. The next day, Matthew is questioning Isabelle about her relationship with Shawn. After giving her lingerie, he tries to get her to manipulate Shawn into letting Richard share power. Back at Sarah's home, the kids meet to try and form a plan. Lindsey asks what each of them can do. One of the boys reveals that he and his sister can make water move, but they must be together. Tyler states that he can manipulate electrical currents, and Maia tells them of her ability. Lindsey is amazed at Maia's precognition and then asks if they're going to be kept at the house for long. Maia replies that they won't be there long, but it's probably not due to an escape. When the hallway door starts to open, the kids run back to their beds. A man enters Maia's room and leaves her new clothes that match the other kids'. Maia then hears screams from Lindsey and watches as the man takes her out of the hall.
At NTAC, the disappearance of Tyler, as well as the disappearances of Olivia and Duncan Germaine (the siblings that can make water move), are reported. Marco arrives and gives Diana some coffee, and after taking a sip, she sets it on a map of the city. It creates a ring stain on the map, and when Tom is shown it, he states, "I'm in the circle." Elsewhere, Richard and Matthew ask Shawn to let Richard share power with him. However, Shawn takes it as a threat. At Sarah's house, Maia asks Tyler if he can make Sarah's car stop if they manage to escape, but Tyler refuses to help. The hallway door then opens, and the man takes Lindsey to her room. Maia goes to check on her and finds that Lindsey has no memory of her. The man soon returns, along with Sarah, and they take Maia. She screams for help, but none of the kids help her.
As Tom and Diana search for Maia, Isabelle shows Shawn her new lingerie. She tells Shawn that if he wants to keep his job, then he can; she can make it happen. However, Shawn considers taking Richard's offer. Meanwhile, Maia, Sarah, and the man are in the kitchen of Sarah's house. Sarah gives Maia a drink and some pills and then tells her to take them. Maia refuses, but Sarah and the man intimidate her into obeying. However, before she can, the lights start flickering. Maia realizes that the kids are helping. The man then collapses, and Sarah is in pain, water emerging from her skin. Outside the house, Diana sees a butterfly design above the home's street address, and she states that Maia is inside. However, when the agents storm in, they discover a real estate agent showing the house to possible buyers.
Meanwhile, Maia runs out the front door of the house and finds herself in the lab where the 4400 were created. Sarah enters and explains that ever since she stepped into her house, she has been in the future. The kids were brought there because their help is needed. A little while later, Maia is on the table, and Sarah is comforting her. Sarah states that the 4400's existence hasn't altered the timeline; the catastrophe still happens. However, they have found a way to fix it by using the kids.
That night (in the present), Shawn signs documents allowing Richard to share power at the 4400 Center. Later, Matthew gives Isabelle a necklace as a "thank you" for getting Shawn to agree with their request. However, Isabelle reveals that she told Shawn to keep his job, and nothing bad happened like Matthew said it would. After stating that she used to be scared of him, Isabelle reveals that he doesn't have any power over her. She then telekinetically tortures him in the air and states that she'll do her own shopping for now on.
In the future, Sarah states that they're sending her and the rest of the kids to a time earlier than when they originally returned. Before doing so, Maia's memories, as well as the memories of the other children, will be wiped. The rest of the world will also forget about her. As Maia disappears into a bright light, her belongings in Diana's house are replaced with other things... read more.

3x3: Being Tom Baldwin recap: As Tom enters an interrogation room containing the now imprisoned T.J. Kim, Diana stops by Kevin Burkhoff's apartment. The lights are out in Burkhoff's place, and she turns them on to wake him up. He is sleeping on the couch and wearing sunglasses. After telling her to turn the lights back off, he reveals to her that he has been having severe migraines. An alarm goes off, telling him that it's time for another injection. Diana gets worried when Burkhoff tells her that he has doubled his daily dosage, but he reassures her.
Meanwhile, Isabelle walks into a lake and drowns. A man in a rowboat sees her body and turns her over, and she returns to life. Elsewhere, after finishing his interrogation of T.J. Kim, Tom pulls out a hidden gun and kills her.
At NTAC, Jarvis informs Diana that T.J. Kim is dead, and Tom was the last one to see her. Diana convinces her to let her talk to Tom first before picking him up. Back at the lake, Isabelle tells Shawn that she wasn't trying to kill herself; she was teaching herself to swim. After she complains that she missed so much when she suddenly grew up, such as learning how to swim or to drive, Shawn volunteers to teach her the basics of swimming. When she later goes to see Richard, she finds him packing clothes. Her father reveals that he's going to put Lily's ashes to rest.
Elsewhere, Tom is at home and is getting out of the shower. Diana enters the room, startling him, and he then sees her gun out. He questions why and seems to have no memory of the shooting. Tom agrees to turn himself in, but shortly after leaving the bathroom to allow him to change, Diana realizes that Tom has escaped out the window. As Tom speeds off in his car, a teen named Boyd Gelder, who disappeared March 3, 2000, calls someone and states that Tom got away.
After informing Jarvis about what happened, Diana gets a call at NTAC from Tom. He refuses to turn himself in and vows to prove his innocence. Diana then visits Marco, who suggests looking at the surveillance footage. However, when the two go to get it, they are told that Marco already obtained the footage!
At the 4400 Center, Shawn is teaching Isabelle how to swim. When he complains about how cold the water is, Isabelle makes it warmer! Matthew Ross then shows up, reminding Shawn about a meeting. Meanwhile, Tom goes to Alana at an art gallery and tells her that he needs her help. Tom pulls on her to come with him, but she resists. He then backs off when her cellphone rings. To her surprise, Tom is on the phone! She says that she doesn't believe him, since Tom is standing right in front of her, but the Tom on the phone starts telling her personal information. The other Tom once again pulls on her to come with him, but the real Tom then arrives and chases him out of the building. However, when he gets outside, he only finds Boyd Gelder. After the teen walks off, Alana and an employee find Tom, who then realizes that the teen was his duplicate.
A little while later, the employee tells them that NTAC agents have arrived, so Tom tells Alana to go home and only answer to him if he gives her a password: Death in Venice, her favorite book. Tom then goes to the 4400 Center, and Shawn lets him use his database to try and find the identity of the teen. Back in Burkhoff's apartment, Diana is worried about Burkhoff and threatens to take him to a hospital. However, he tells her he wants to show her something. He then stabs his hand with a scalpel, and to Diana's amazement, his wound instantly heals!
The next day, Shawn tries teaching Isabelle to drive. When he asks if there is anything on her list of rites of passage that doesn't involve risk of bodily harm, she suggests having sex. He tells her that he doesn't want to because he doesn't want to take advantage of her, nor does he want to make Richard angry. Meanwhile, Tom calls Diana and informs her that he has located the 4400 who has been impersonating him. She departs to join Tom, but along the way, she runs into Marco. He asks why she is leaving so suddenly, and she explains where she is going. However, it appears that it isn't actually Marco!
Near Boyd's home, two Dianas arrive to meet Tom! One pulls out a gun and starts shooting, so Tom and the real Diana return fire. The impostor runs, and the duo gives chase. However, Boyd disappears near a children's soccer game. Diana tells Tom that he can return to NTAC now that she knows that he is telling the truth, but Tom doesn't believe that a testimony from his partner will be enough proof. The two then set off to locate Boyd.
As Isabelle is told by Richard over the phone that she is too young to be thinking about sex, Tom and Diana visit Boyd's mother. She believes that her son is on a ski trip with friends, but the agents inform her that he isn't. They then convince her to contact Boyd and to get him to go to a location. However, as Tom and Diana wait for him to arrive, they notice NTAC vans. Thinking the ruse has been blown, the duo departs.
Alana is shocked when Tom arrives at the house, since NTAC agents are monitoring the place. He tells her that the agents aren't there and gives her the password. However, she is suspicious since he doesn't have his key, so Boyd kicks the door in. Alana runs, but Boyd pulls out a gun. The real Tom gets a call from Boyd, who tells him that he has written a suicide note for him. Tom refuses to sign, but Boyd threatens to kill Alana. Meanwhile, at the 4400 Center, Matthew Ross gives Isabelle a new dress. After telling her that he thinks it's good that she's spending time with Shawn, he suggests doing it even more. Isabelle informs him that what she's doing isn't for him, and Matthew claims that she and Shawn will eventually be "on opposite sides of a very large, ideological divide." Because of this, she must not let her emotions run too deep, or it will make things more difficult later. As he leaves, he tells Isabelle that her dress doesn't match her eyes and that she should take care of that. She then changes her eye color to green! Elsewhere, in a cemetary, Richard scatters Lily's ashes on the grave of her grandmother, the Lily he first loved.
In Tom's house, Alana tries to reason with Boyd, but to no AVAIL. They then hear something. With Boyd distracted by the noise, Alana smashes a vase over his head. She then runs into the kitchen, where the real Tom is. Tom and his doppelganger then fight, while Alana grabs the gun. The two Toms start telling her personal information in order to convince her that they are the true Tom. One bit of information is about her son Billy, who died in a car crash. Alana then notices that one of them is bleeding from the head, and she remembers hitting Boyd with a vase. She orders Boyd to get on his knees, and after he does so, Tom handcuffs him. When Boyd returns to his true form, Alana is shocked to see that he is a teenager. As he is being taken away, he tells her that he's a soldier, and there are more of them everyday.
Richard returns to the 4400 Center and thanks Shawn for watching after Isabelle. He admits to Shawn that he's afraid that people will see Isabelle as a beautiful woman and forget that she's only a child inside. However, it seems more like a message. Later, as Diana gives the even weaker Burkhoff another dose, Shawn returns to his room and finds Isabelle waiting for him in her new dress. She walks forward and has her first kiss with him, and the two start making out... read more.

1x1: The Return recap: March 3, 1946. Maia, an eight years old blonde girl, is at a picnic with her parents in California. Bored, she asks them to let her wander the surrounding area. As she picks up some flowers, a bright light appears over her and disappears with the young child... read more.